title: Single-cell transcriptome analysis reveals the dynamics of human immune cells during early fetal skin development

city: Guangzhou

first: Yingping

last: Xu

state: Guangdong

address: LuJing Road

institute: Sourthern Medical University

summary: The immune system of skin develops in stages in mice. However, the developmental dynamics of immune cells in human skin remains elusive. Here we perform transcriptome profiling of CD45+ hematopoietic cells in human fetal skin at an estimated gestational age of 10–17 weeks by single-cell RNA sequencing. A total of 13 immune cell types are identified. Skin macrophages show heterogeneity and dynamic over the course of skin development. A major shift in lymphoid cell developmental states occurs from the first to the second trimester that implied an in situ differentiation process. Gene expression analysis reveals a typical developmental program in immune cells in accordance with their functional maturation, possibly involving metabolic reprogramming. Finally, we identify transcription factors (TFs) that potentially regulate cellular transitions by comparing TFs and TF-target gene networks. These findings provide detailed insight into how the immune system of the human skin is established during development

first: Jun

last: Zhang

first: Yongfei

last: Hu

first: Xuefei

last: Li

first: Lihua

last: Sun

first: Yu

last: Peng

first: Yuzhe

first: Bing

last: Liu

first: Zhilei

last: Bian

first: Zhili

last: Rong


title: The role of Vitamin C and TET dioxygenases in genome-wide features of regulatory T cells

status: Public on Jul 19 2021

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Cir

department: Signaling and Gene Expression

country: USA

institute: La Jolla Institute for Allergy and Immunology

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: MeRIPseq of Toxoplasma gondii

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

summary: Toxoplasma gondii is an obligate intracellular parasite that can cause serious opportunistic disease in the immunocompromised or through congenital infection. To progress through its life cycle, Toxoplasma relies on multiple layers of gene regulation that includes an array of transcription and epigenetic factors. Over the last decade, the modification of mRNA has emerged as another important layer of gene regulation called epitranscriptomics. Here, we report that epitranscriptomics machinery exists in Toxoplasma, namely the methylation of adenosines (m6A) in mRNA transcripts. We identified novel components of the m6A methyltransferase complex and determined the distribution of m6A marks within the parasite transcriptome. m6A mapping revealed the modification to be preferentially located near transcription termination sites within the consensus sequence, YGCAUGCR. Knockdown of the m6A writer enzyme METTL3 resulted in diminished m6A marks, loss of a target transcript, and a complete arrest of parasite replication. Furthermore, we examined the two proteins in Toxoplasma that possess YTH domains, which bind m6A marks, finding them to be integral members of the cleavage and polyadenylation machinery that catalyzes the 3’-end processing of pre-mRNAs. Together, these findings establish that the m6A epitranscriptome is essential for parasite viability by contributing to the processing of mRNA 3’-ends.

overall_design: determination of m6A epitranscriptome in 3 replicates each of Toxoplasma gondii tachyzoites and early bradyzoites

middle: J

first: Leah

middle: R

last: Padgett

first: Matheus

middle: S

last: Bastos

first: William

last: Sullivan Jr


title: FOXC2 controls adult lymphatic endothelial specialization, function and gut lymphatic barrier preventing multi-organ failure

status: Public on Jul 16 2021

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics


title: Transcriptomes of adult mesentery and lung tissues from wildtype and Foxc2lecKO mice

summary: Bulk RNA sequencing of mesentery and lung tissues from adult willdtype and Foxc2lecKO mice

overall_design: Methods: The samples were sequenced using a single-end configuration at the Lausanne Genomic Technologies Facility (https://wp.unil.ch/gtf/), each sample being sequenced on three separate lanes to increase coverage per sample. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated by the Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mis-match was allowed for index sequence identification.

first: A

last: González-Loyola

first: T

middle: V

last: Petrova


title: Abrupt and altered cell-type-specific DNA methylation profiles in blood during Acute HIV infection persists despite prompt initiation of ART

status: Public on Jul 15 2021

city: New York

last: Corley

state: NY

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

institute: Weill Cornell Medicine

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of monocytes and CD4+ T cells during acute HIV infection and following ART.

overall_design: Bisulfite-converted DNA from FACS-sorted cells were hybridized to the Illumina MethylationEPIC Beadchip.

first: Lishomwa

last: Ndhlovu


title: Combinatorial treatment recovers altered gene expression in cortex of CD animals

city: Barcelona

first: Victoria

last: Campuzano

state: Barcelona

address: Casanovas, 143

department: Biomedicina

country: Spain

institute: Universitat de Barcelona

summary: To identify the molecular causes that could be related to the improvement in certain aspects of the behavioral phenotype in double-treated animals, we searched for differentially expressed genes (DEG) by performing an RNA-seq analysis of cerebral cortex from VER+CUR-treated CD mice versus vehicle-treated CD and WT mice.

overall_design: Cortical mRNA profiles of 16 weeks old treated and untreated wild type (WT) and CD mice


title: Transcriptomes of adult lymphatic endothelial cells from wildtype and Foxc2lecKO mice

summary: Single cell RNA sequencing of mesenteric lymphatic endothelial cells from adult willdtype and Foxc2lecKO mice

overall_design:
Methods: single cell RNAseq profiles of  lymphatic endothelial cells sorted from WT and Foxc2lecKO  were generated by 10x sequencing, in triplicate. The sequencing libraries prepared following the manufacturer’s recommendations (Chromium Single Cell 3ʹ GEM Kit v3). Briefly, an emulsion encapsulating single cells, reverse transcription reagents and cell barcoding oligonucleotides was generated. After the actual reverse transcription step, the emulsion was broken and double stranded cDNA generated and amplified in a bulk reaction for 12 PCR cycles. This cDNA was fragmented, a P7 sequencing adaptor ligated, and a 3’ gene expression library generated by a 14 cycles PCR amplification.
Libraries were quantified by a fluorimetric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies). Cluster generation was performed with 1.4nM of an equimolar pool from the resulting libraries, including 10% PhiX spike, using the Illumina HiSeq 3000/4000 PE Cluster Kit reagents (Illumina). Sequencing was performed on 2 runs in the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents (Illumina) according to Illumina 10X Genomics recommendations. Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina) and primary data analysis performed with the Cell Ranger Gene Expression pipeline (version 3.1.0, 10X Genomics). A minimum of 33.000 reads/ cell were obtained and 18.271 genes on average were detected.


title: Extracellular CIRP Induces an Inflammatory Phenotype in Pulmonary Fibroblasts via TLR4

city: Manhasset

first: Siavash

last: Bolourani

address: 350 Community Dr

department: Molecular Medicine

institute: Feinstein Institutes for Medical Research

summary: The wild type (WT) and TLR4 -/- pulmonary fibroblasts were treated with phosphate-buffered saline (PBS), 1 µg/mL recombinant mouse (rm) CIRP, 2 ng/mL rmTGF-ß1 (R&D Systems), or rmCIRP plus rmTGF-ß1. The cell lysates collected at 24 hours were used for high throughput mRNA sequencing.

overall_design: mRNA profile of WT and TLR4 -/- pulmonary fibroblasts.

first: Ping

last: Wang

first: Max

last: Brenner

first: Ezgi

last: Sari


title: Gene expression profiling in RagC Q119L murine B220+ lymphoma cells

status: Public on Jul 13 2021

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

institute: CNIO

summary: Gene expression by RNAseq  in murine B220+ from VavP-Bcl2/RagC Q119L/+ and VavP-Bcl2/RagC +/+ lymphomas

overall_design: Using RNA-seq we profiled murine B220+ purified cells from VavVPBcl2/RagC Q119L/+(n=5) and VavVPBcl2/RagC +/+ lymphomas (n=4)

first: Ana

last: Ortega-Molina

last: Graña-Castro

first: Alejo

last: Efeyan


title: Transcriptional Changes Associated with Acute to Chronic Stage Muscle Adaptations in a Model of Rotator Cuff Tendon Tear

status: Public on Jul 14 2021

first: Samuel

middle: Richard

last: Ward

state: CA

address: 9500 Gilman Drive (0863)

department: Orthopaedic Surgery, Radiology, and Bioengineering

institute: University of California San Diego

summary: In this study, we collected rabbit supraspinatus muscle tissue with higher temporal resolution (1, 2, 4, 8, 16 weeks) post-tenotomy (n=6/group), where muscle degeneration occurs at later time points, to determine if transcriptional changes occur. RNA sequencing and analyses were performed using standard techniques to identify a transcriptional timeline of rotator cuff muscle changes and related morphological sequelae.

overall_design: rotator cuff muscle mRNA after tenotomy injury at 1, 2, 4, 8, 16 weeks post-tenotomy

first: Laura

last: Vasquez-Bolanos

middle: C

last: Gibbons

first: Severin

last: Ruoss

first: Isabella

middle: T

last: Wu

first: Sydnee

middle: A

last: Hyman

first: Mario

last: Vargas-Vila

first: Mary

last: Esparza

first: Donald

last: Fithian

first: Anshuman

last: Singh

first: Chanond

last: Nasamran

first: Kathleen

last: Fisch


title: RNA sequencing of Mtb H37Rv, MtbΔsufR and sufR complemented mycobacterium tuberculosis strains  upon treatment with 0.5 mM DETA-NO.

city: Bengaluru

first: Amit

state: KARNATAKA

address: Sir CV Raman Road

department: Microbiology and Cell Biology

country: India

institute: Indian Institute of Science

summary: Fe-S cluster proteins are involved in fundamental processes such as electron transfer, gene regulation, and DNA repair in diverse bacteria. Since Fe-S clusters are susceptible to damage by oxidative and nitrosative stress conditions, bacteria harbour systems such as ISC (iron-sulfur cluster assembly) and SUF (sulfur mobilization) to regulate Fe-S homeostasis. Fe-S cluster production is tightly regulated so as to promote Fe-S formation when the necessity for clusters is heightened (e.g., ROI/RNI/iron limitation) and to limit unnecessary production when the demand is low (e.g., hypoxia). Deregulation of Fe-S cluster biogenesis can lead to the accumulation of metabolic poisons such as polysulfides and reactive oxygen species. The human pathogen, Mycobacterium tuberculosis (Mtb) exploits several Fe-S containing proteins to maintain cellular homeostasis and survival in an antagonistic host environment. The Mtb genome encodes an atypical Suf system (Rv1460-Rv1466;sufRBDCSUT) as the only complete Fe-S cluster biogenesis machinery. Expression of sufR and the complete operon was shown to be upregulated upon exposure to nitrosative stresses. Thus, we did transcriptomic study of sufR deleted strain upon exposure to 0.5 mM DETA-NO to study comprehensively the suf regulon in response to ROI/RNI stress and what are the underlying regulatory mechanisms.

overall_design: The study involves profiling of mRNA signatures of these strains to show the important role of first gene of suf operon (sufR) to facilitate regeneration of Fe-S clusters during recovery from nitrosative stress. Wt Mtb H37Rv, MtbΔsufR and sufR complemented  strains were grown till early log phase and exposed to 0.5 mM DETA-NO for 4 hours at 37 degree at 180rpm. Three independent experiments were done for each of the strain, respectively.

first: K

last: Anand

first: N

last: Malhotra

first: A

last: Tripathi

last: Seshasayee


title: Gene expression profiling in RagC Q119L germinal centre B cells

first: Osvaldo

last: Graña

summary: Gene expression by RNAseq  in murine  RagC Q119L/+ and RagC +/+  germinal centre B cells

overall_design: Using RNA-seq we profiled germinal centre B (GC B) cells purified cells RagC Q119L/+ (n=5) and RagC +/+ mice (n=4)

first: Ana

last: Ortega-Molina

last: Graña-Castro

last: Efeyan


title: Gene expression profiling in RagC Q119L murine germinal centre B cells and B220+ lymphoma cells


title: Severe deficiency of voltage-gated sodium channel NaV1.2 elevates neuronal excitability in adult mice

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

summary: Scn2a encodes voltage-gated sodium channel NaV1.2, a main mediator of neuronal action potential firing. The current paradigm suggests that NaV1.2 gain-of-function variants enhance neuronal excitability resulting in epilepsy, whereas NaV1.2 deficiency impairs excitability contributing to autism. This paradigm, however, does not explain why 20~30% of patients with NaV1.2 deficiency still develop seizures. Here we report a counterintuitive finding that severe NaV1.2 deficiency results in increased neuronal excitability. Using a unique NaV1.2-deficient mouse model, we found enhanced intrinsic excitabilities of principal neurons in the prefrontal cortex and striatum, brain regions known to be involved in Scn2a-related seizures. This increased excitability is autonomous, and is reversible by the genetic restoration of Scn2a expression in adult mice. RNA-sequencing revealed that the downregulation of multiple potassium channels including KV1.1, and KV channel openers alleviated hyperexcitability of NaV1.2-deficient neurons. This unexpected neuronal hyperexcitability may serve as a cellular basis underlying NaV1.2 deficiency-related seizures.

overall_design: Since Scn2a null (100% knockout) is lethal, we thus generated a novel NaV1.2-deficient mouse model via a gene-trap strategy . Using this unique mouse model, we investigated how severe NaV1.2 deficiency affects neuronal excitabilities in principal neurons of the cortico-striatal circuit.

first: Jingliang

last: Zhang

first: Xiaoling

last: Chen

first: Muriel

last: Eaton

first: Jiaxiang

first: Zhixiong

last: Ma

first: Shirong

last: Lai

first: Anthony

last: Park

first: Talha

last: Ahmad

first: Zhefu

last: Que

first: Ji

middle: H

last: Lee

first: Tiange

last: Xiao

first: Yuansong

last: Li

first: Yujia

last: Wang

first: Maria

middle: I

last: Olivero-Acosta

first: James

last: Schaber

first: Krishna

last: Jayant

first: Chongli

last: Yuan

first: Zhuo

last: Huang

last: Lanman

first: William

last: Skarnes

first: Yang

last: Yang


title: The p53 transcriptional response across tumor types reveals core and outcome-specific signatures modulated by cis-regulatory lncRNAs

city: LOS ANGELES

first: Jesse

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles


title: The p53 transcriptional response across tumor types reveals core and outcome-specific signatures modulated by cis-regulatory lncRNAs [RNA-seq]

summary: The p53 pathway is a universal tumor suppressor mechanism but the differences of the p53 transcriptional response to oncogenic stress across different tumor types are poorly understood. Using a panel of murine cancer cell lines, we observed that the majority of p53-bound sites were tumor type-specific. Analysis of common p53 targets defined a small but robust core signature and revealed a senescence-specific repression geneset. Characterization of novel transcripts identified p53-induced lncRNAs, which frequently associated with chromatin and regulated their neighboring mRNAs. These findings shed light on the unique and shared p53 transcriptional signatures across different contexts and clarify the contributions of lncRNAs to the p53 transcriptome.

overall_design: RNA seq of K-rasG12D; p53LSL/LSL; Rosa26-CreERT2 (KPR) cell lines isolated from murine lung adenocarcinomas (LA), sarcomas (SA), and lymphomas (LY)


title: RNA-seq analysis of MmuPV1 infected mouse warts and control tissues

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

institute: National Cancer Institute

summary: We perfomed RNA-seq analysis using MmuPV1 infected mouse warts and control tissues for MmuPV1 integration and host gene expression analyses

overall_design: Athymic FoxN1nu/nu mice were experimentally infected with quasivirions containing MmuPV1 synthetic genome at three anatomical sites (ear, muzzle, and tail). The warts tissues formed at the infection sites were harvested together with uninfected control ears for total RNA extraction and RNA-seq using Illumina platform was performed on ribo-minus total RNA. MmuPV1 integration were examined subsequently.

first: Lulu

last: Yu

first: Vladimir

last: Majerciak

first: Alexei

last: Lobanov


title: A novel mechanism of Cannabidiol in suppressing hepatocellular carcinoma by inducing GSDME dependent pyroptosis

city: wenzhou zhejiang province china

first: Fugen

last: ShangGuan

address: Nanbaixiang Street, Ouhai District

country: China

institute: The First Affiliated Hospital of Wenzhou Medical University

summary: Cannabidiol (CBD), a phytochemical derived from Cannabis sativa L., has been demonstrated to exhibit promising anti-tumor properties in multiple cancer types. However, the effects of CBD on Hepatocellular carcinoma cells (HCC) remains unknown. We have shown that CBD effectively suppresses HCC cell growth in vivo and in vitro, and induced HCC cell pyroptosis in a caspase-3/GSDME-dependent manner. We further demonstrated that accumulation of Integrative Stress Response (ISR) and mitochondrial stress may contribute to the initiation of pyroptotic signaling by CBD. Simultaneously, CBD can repress aerobic glycolysis through modulation of the ATF4-IGFBP1-Akt axis, due to the depletion of ATP and crucial intermediate metabolites. Collectively, these observations indicate that CBD could be considered as a potential compound for HCC therapy.

overall_design: The mRNA profiles of HepG2 and MHCC97H CBD exposed cells were generated by deep sequenceing，using illumina GAILX. And RNA-seq data was generated by Novogene, china.

last: Guan

first: Hongfei

last: Zhou

first: Shanshan

last: Wu


title: Transcriptome analysis of D. melanogaster developed in conditions of low radiation background laboratory and control group

city: Dubna

first: Mikhail

last: Zarubin

address: Russia, Moscow region, Dubna, Juliot Curie, 20

country: Russia

institute: Joint Institute for Nuclear Research

summary: The goal of our study was to determine effects of natural radiational background deprivation in conditions of DULB-4900 lab (BNO INR RAS, Neutrino) for multicellullar organism D. melanogaster (Oregon line) through transcriptome profiling (RNA-seq)

overall_design: Total RNA profiles of 3-day old adult D. melanogaster Oregon line (Or)

first: Elena

last: Kravchenko


title: Blood-Tumor overlapping TCR repertoire predicts the clinical responses of PD-1 blockade in patients with gastrointestinal cancer

city: Noda

first: Hiroyasu

last: Aoki

state: Chiba

address: 2669 Yamazaki

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science


title: The p53 transcriptional response across tumor types reveals core and outcome-specific signatures modulated by cis-regulatory lncRNAs [ChIP-seq]

overall_design: p53 ChIPseq of K-rasG12D; p53LSL/LSL; Rosa26-CreERT2 (KPR) cell lines isolated from murine lung adenocarcinomas (LA), sarcomas (SA), and lymphomas (LY)


title: RNA-seq analysis in HEK293T WT and SCARNA15-KO cells

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

summary: Small Cajal body-specific RNAs (scaRNA) are conserved small noncoding RNAs that guide post-transcriptional modification of spliceosomal RNA (snRNA), a key step for accurate spliceosome biogenesis and function. Despite scaRNA expression being altered in cancer, how this impacts pre-mRNA splicing remains mostly unexplored. Here, we uncovered SCARNA15 as a critical regulator of cancer-promoting alternative splicing (AS) and stress adaptation. Our scaRNA expression analysis reveals a remarkable SCARNA15 upregulation during malignant transformation, which ensures pseudouridylation (Y) within a functional region of the U2 snRNA. This fines tune AS of distinct transcripts encoding oncoproteins and tumor-suppressors including central p53 regulators. Critically, SCARNA15 loss leads to aberrant p53 hyperactivation and impaired cancer cell survival in response to oxidative stress. Accordingly, SCARNA15-mediated redox homeostasis impacts cancer cell survival, movement and anchorage-independent growth. In sum, these findings highlight a functional role for SCARNA15 and Y in directing cancer-promoting AS programs in human cells.

overall_design: 3 sets of samples including HEK293T WT and HEK293T SCARNA15-KO clone1 were included in the study. Each sample was biologically independent, matched triplicates.

first: Giulia

last: Beneventi

first: Cristian

last: Bellodi


title: Blood-Tumor overlapping TCR repertoire predicts the clinical responses of PD-1 blockade in patients with gastrointestinal cancer[RNA-Seq]

summary: As the anti-PD-1 monoclonal antibody (mAb) becomes to be used in many types of cancers, the needs for the predictive biomarker of PD-1 blockade are growing. T cell receptor (TCR) repertoire—which reflects the anti-tumor T-cell responses based on the antigen specificity—is a potential biomarker of cancer immunotherapy. Here, we analyzed the TCR repertoire of patients with advanced gastrointestinal cancer and explored its association with clinical responses.

overall_design: Eight patients with advanced gastrointestinal cancer were treated with an anti-PD-1 monoclonal antibody (nivolumab) every 3 weeks until disease progression. The TCR repertoire of the peripheral blood CD4+ and CD8+ T cells was analyzed once before and three times after the initiation of treatment, whereas in case of tumor biopsy it was analyzed before and after 6 weeks of initiation of the treatment.

first: Satoshi

last: Ueha

first: Yoshiaki

last: Nakamura

first: Shigeyuki

last: Shichino

first: Hiromichi

last: Nakajima

first: Manami

last: Shimomura

first: Akihiro

last: Sato

first: Tetsuya

last: Nakatsura

first: Takayuki

last: Yoshino

first: Kouji

last: Matsushima


title: LB001: The ALPK1 pathway drives the inflammatory response to Campylobacter jejuni in human intestinal epithelial cells

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

summary: The Gram-negative bacterium Campylobacter jejuni is a major cause of foodborne disease in humans. After infection, C. jejuni rapidly colonizes the mucus layer of the small and large intestine and induces a potent pro-inflammatory response characterized by the production of a large repertoire of cytokines, chemokines, and innate effector molecules, resulting in (bloody) diarrhea. The virulence mechanisms by which C. jejuni causes this intestinal response are still largely unknown. Here we show that C. jejuni releases a potent pro-inflammatory compound into its environment, which activates an NF-B-mediated pro-inflammatory response including the induction of CXCL8, CXCL2, TNFAIP2 and PTGS2. This response was dependent on a functional ALPK1 receptor and independent of Toll-like Receptor and Nod-like Receptor signaling. Chemical characterization, inactivation of the heptose-biosynthesis pathway by the deletion of the hldE gene and in vitro engineering identified the released factor as the LOS-intermediate ADP-heptose and/or related heptose phosphates. During C. jejuni infection of intestinal cells, the ALPK1-NF-kB axis was potently activated by released heptose metabolites without the need for a type III or type IV injection machinery. Our results classify ADP-heptose and/or related heptose phosphates as a major virulence factor of C. jejuni that may play an important role during Campylobacter infection in humans.

overall_design: The microarray experiment was performed 4 times, as a direct comparison between HeLa 57A cells stimulated with  C. jejuni-released ADP-heptose and mock stimulated HeLa 57A cells. Opposite labeling of two of four sample sets generated a balanced dye-swap design. Microarrays used were human whole genome gene expression microarrays V2 (Agilent, Belgium) representing 34127 H. sapiens 60-mer probes in a 4x44K layout.

first: Lieneke

last: Bouwman

first: Marcel

last: de Zoete

first: Jiannan

last: Cui

first: Jos

middle: P

last: van Putten

first: Kristel

last: van Rooijen

first: Carlos

middle: G

last: Voogdt

first: Coco

last: Duizer


title: Targeted DNA-seq analysis of MmuPV1 infected mouse warts and uninfected control tissues

first: Zhi-Ming

last: Zheng

summary: We perfomed Targeted DNA-seq analysis using MmuPV1 infected mouse warts and uninfected control tissues for MmuPV1 integration analyses

overall_design: Athymic FoxN1nu/nu mice were experimentally infected with quasivirions containing MmuPV1 synthetic genome. The warts tissues formed at the infection sites were harvested together with uninfected control tissues for DNA extraction and DNA-seq using Illumina platform. MmuPV1 integration were examined subsequently.

first: Lulu

last: Yu

first: Vladimir

last: Majerciak

first: Alexei

last: Lobanov


title: Blood-Tumor overlapping TCR repertoire predicts the clinical responses of PD-1 blockade in patients with gastrointestinal cancer [TCR-Seq]

first: Hiroyasu

last: Aoki

first: Satoshi

last: Ueha

first: Yoshiaki

last: Nakamura

first: Shigeyuki

last: Shichino

first: Hiromichi

last: Nakajima

first: Manami

last: Shimomura


title: Effects of Aflibercept administration at 25 mg per kg body weight in retinas of mice subjected to the oxygen-induced retinopathy protocol [P19]

city: Cambridge

first: Jesus Eduardo

last: Rojo Arias

address: Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

summary:
We aimed at identifying the regulatory network of Aflibercept in the context of pathological neovascularization by using the oxygen-induced retinopathy mouse model as a surrogate of proliferative diabetic retinopathy
Total RNA was collected from entire retinal cups dissected from 19-days old mice subjected to the oxygen-induced retinopathy protocol and subsequently injected with Aflibercept either on postnatal days 13 and 15 (OIR+AFLx2) or on postnatal days 13, 15 and 17. Non-injected OIR littermates (OIR) and age-matched mice housed in normoxic conditions (normoxia) were used as controls.

overall_design: Four treatments were considered, namely normoxic controls, OIR mice, OIR mice injected twice with Aflibercep (OIR+AFLx2), and OIR mice injected three times with Aflibercept (OIR+AFLx3). Each group contained three biological replicates, i.e. three mice. All RNA samples were collected on postnatal day 19. Thus, 12 samples were analyzed in total: 1 time-point, 4 treatments, and 3 replicates per treatment. Each sample consists of total RNA isolated from the 2 entire pooled retinas of 1 mouse.

first: Jesus

middle: E

first: József

last: Jászai


title: Early Transcriptional Liver Signatures in Experimental Visceral Leishmaniasis

status: Public on Jul 12 2021

city: La Laguna

first: Emma

last: Carmelo

state: SANTA CRUZ DE TENERIFE

address: C/ Astrofisico Francisco Sanchez s/n, Campus de Anchieta

department: University Institute of Tropical Diseases and Public Health

institute: University of La Laguna

summary: Transcriptional analysis of complex biological scenarios has been used extensively, even though sometimes the results of such analysis may prove imprecise or difficult to interpret due to an overwhelming amount of information. In this study, a large-scale real-time qPCR experiment was coupled to multivariate statistical analysis in order to describe the main immunological events underlying the early L. infantum infection in livers of BALB/c mice. High-throughput qPCR was used to evaluate the expression of 223 genes related to immunological response and metabolism 1, 3, 5, and 10 days post infection. This integrative analysis showed strikingly different gene signatures at 1 and 10 days post infection, revealing the progression of infection in the experimental model based on the upregulation of particular immunological response patterns and mediators. The gene signature 1 day post infection was not only characterized by the upregulation of mediators involved in interferon signaling and cell chemotaxis, but also the upregulation of some inhibitory markers. In contrast, at 10 days post infection, the upregulation of many inflammatory and Th1 markers characterized a more defined gene signature with the upregulation of mediators in the IL-12 signaling pathway. Our results reveal a significant connection between the expression of innate immune response and metabolic and inhibitory markers in early L. infantum infection of the liver.

overall_design: 48 BALB/c  mice (14-15 weeks old) were randomly separated in two groups: (i) 24 control mice and (ii) 24 mice  that were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein. Mice were euthanized by cervical dislocation and livers were removed and immediately stored in RNAlater at -70°C. After RNA extraction and reverse transcription, the expression of 223 genes related with immune system was determined by high-throughput qPCR using QuantStudio 12K Flex Real-Time PCR System.

first: Génesis

last: Palacios

first: Raquel

last: Diaz-Solano

first: Basilio

last: Valladares

first: Roberto

last: Dorta-Guerra


title: The prostaglandin D2 receptor CRTH2 suppresses epithelial responses during intestinal helminth infection

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: Single cell RNAseq comparing intestinal samples of WT and CRTH2-KO samples.

overall_design: Three WT mice intestines and three CRTH2-KO mice intestines were dissected, dissociated, and single cell RNA-seq was performed.

first: Elia

middle: D

last: Tait Wojno

first: Matt

last: Kanke


title: Role of hypothalamic MAPK/ERK signaling in diabetes remission induced by the central action of fibroblast growth factor 1

city: Copenhagen

first: Tune

middle: Hannes

last: Pers

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Basic Metabolic Research

country: Denmark

institute: University of Copenhagen

summary: The capacity of the brain to elicit sustained remission of hyperglycemia in rodent models of type 2 diabetes (T2D) following intracerebroventricular (icv) injection of fibroblast growth factor 1 (FGF1) is well established.  Here, we show that icv FGF1 injection induces signaling by extracellular signal-regulated kinases 1 and 2 (ERK1/2), members of the mitogen-activated protein kinase (MAPK) family in the hypothalamus, and that this activation persists for at least 24h. Further, we show that in diabetic Lepob/ob mice, this prolonged response is required for the sustained antidiabetic action of FGF1, since it is abolished by sustained (but not acute) pharmacologic blockade of hypothalamic MAPK/ERK signaling. We also demonstrate that FGF1 R50E, a FGF1 mutant that activates FGF receptors but induces only transient hypothalamic MAPK/ERK signaling, elicits transient but not sustained glucose lowering. These data implicate sustained hypothalamic MAPK/ERK signaling in the mechanism underlying diabetes remission induced by icv FGF1.

overall_design: single-cell RNA sequencing (10X genomics Chromium system) and bulk RNA-sequencing

first: Marie

last: Bentsen

first: Dylan

middle: M

last: Rausch

first: Jenny

last: Brown

first: Jarrad

last: Scarlett

first: Michael

middle: W

last: Schwartz


title: NAT10-mediated N4-acetylcytidine of RNA Contributes to Post-transcriptional Regulation of Mouse Oocyte Maturation In Vitro

status: Public on Jul 11 2021

city: Guangzhou

first: Yuting

last: Xiang

state: China

address: No. 26, Yuancunerheng Road, Tianhe District, Guangzhou, China

institute: Reproductive Medicine Center, Sixth Affiliated Hospital of Sun Yat-Sen University

summary: N4-acetylcytidine (ac4C), a newly identified epigenetic modification within mRNAs, has been characterized as a crucial regulator of mRNA stability and translation efficiency. And NAT10 is the only known RNA acetyltransferase. In our study, we documented the down-regulated expression of both ac4C and NAT10 during meiotic maturation of mouse oocytes. NAT10 knockdown resulted in ac4C reduction and impaired mouse oocyte maturation in vitro. These results indicated that NAT10-mediated ac4C modification plays a critical regulatory role in oocyte meiotic maturation. We further performed high-throughput sequencing with NAT10-overexpressed HEK293T cells and NAT10-binding transcripts to investigate the genes modulated by NAT10-mediated ac4C modification.

overall_design: NAT10-overexpressed HEK293Tcells and NAT10-binding Transcripts

first: Chuanchuan

last: Zhou

first: Yanyan

last: Zeng

first: Qi

last: Guo

first: Jiana

last: Huang

first: Taibao

last: Wu

first: Jiawen

last: Liu

first: Qiqi

last: Liang

first: Haitao

first: Xiaoyan


title: The WDR5-H3K4me3 epigenetic axis regulates OPN expression to compensate PD-L1 function to promote pancreatic cancer immune escape

status: Public on Jul 09 2021

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: The WDR5-H3K4me3 epigenetic axis regulates OPN expression to compensate PD-L1 function to promote pancreatic cancer immune escape [RNA-seq]

summary: Two orthotopic pancreatic tumor mouse models were used for ChIP-Seq and RNA-Seq to identify genome-wide dysfunction of H3K4me3 and gene expression. Mouse pancreatic tumors have a genome-wide increase in H3K4me3 deposition as compared to normal pancreas. Osteopontin (OPN) and its receptor CD44 were identified being up-regulated in pancreatic tumors by their promoter H3K4me3 deposition. OPN protein is increased in both tumor cells and tumor-infiltrating immune cells in human pancreatic carcinoma and is inversely correlated with pancreatic cancer patient survival. OPN is primarily expressed in tumor cells and monocytic myeloid-derived suppressor cells (M-MDSCs), whereas PD-L1 is expressed in tumor cells, M-MDSCs, polymorphonuclear MDSCs (PMN-MDSCs) and tumor-associated macrophages. WDR5 is essential for H3K4me3-specific histone methyltransferase activity and OPN expression in tumor cells and MDSCs. Pharmacological inhibition of WDR5 significantly decreased OPN protein level, suppressed pancreatic tumor growth, and significantly increased efficacy of anti-PD-1 immunotherapy in suppression of pancreatic tumor growth in vivo.

overall_design: Total RNA was isolated from normal C57BL/6 mouse pancreas, PANC02-H7, and UN-KC-6141 tumors from tumor-bearing mice. The RNA was used for RNA-Seq. The gene expression profiles between normal mouse pancreas and orthotopic pancreatic tumors were compared, and differentially expressed genes were identified.

first: Chunwan

last: Lu

first: Kebin


title: Transcriptomic analysis of embryonic hearts with conditional deletion of Wt1

status: Public on Jul 10 2021

city: Nalaga

first: Ramon

last: Muñoz-Chápuli

address: Campus de Teatinos

institute: University of Malaga

summary: We performed a conditional ablation of Wt1 in the myocardium of mice embryos. RNASeq analysis identified differential expression of 137 genes in the E13.5 mutant heart as compared to controls. GO functional enrichment analysis suggested that both calcium ion regulation and modulation of potassium channels are deeply altered in the mutant myocardium

overall_design: mRNA profiles of E13.5 wild type (WT) and TnnT2Cre;Wt1flox mutant embryos

first: Ramón


title: Intercellular cGAMP transmission induces innate immune activation and tissue inflammation in Trex1 deficiency

city: Bonn

first: Lino

middle: Lars

last: Teichmann

address: Venusberg-Campus 1

department: Department of Medicine III

country: Germany

institute: University Hospital Bonn

summary: Intercellular transmission of the second messenger 2′,3′‐cGAMP, synthesized by the viral DNA sensor cGAMP synthase (cGAS), is a potent mode of bystander activation during host defense. However, whether this mechanism also contributes to cGAS-dependent autoimmunity remains unknown. Here, using a murine bone marrow transplantation strategy, we demonstrate that, in Trex1-/--associated autoimmunity, cGAMP shuttling from radioresistant to immune cells induces NF-κB activation, interferon regulatory protein 3 (IRF3) phosphorylation and subsequent interferon signaling. cGAMP travel prevented myeloid cell and lymphocyte death, promoting their accumulation in secondary lymphoid tissue. Nonetheless, it did not stimulate B cell differentiation into autoantibody-producing plasmablasts or aberrant T cell priming in the steady state. Although cGAMP-mediated bystander activation did not induce spontaneous organ disease, it did trigger interface dermatitis after UV light exposure, similar to cutaneous lupus erythematosus. These findings reveal that, in Trex1-deficiency, intercellular cGAMP transfer propagates cGAS signaling and, under conducive conditions, causes tissue inflammation.

overall_design: Total RNA was isolated from single-cell suspensions of bone marrow from Cgas-/- mice and Trex1-/-;Sting1gt/gt mice (called dKO). In addition, total RNA was isolated from single-cell suspensions of spleens from dKO mice 12 weeks after they were lethally irradiated and transplanted with Cgas-/- or dKO bone marrow. 3'-mRNA Seq was performed on an Illumina HiSeq 2500.

first: Bianca

middle: B

last: Jütte

first: Ruth-Miriam

last: Koerber

first: Claus

last: Gräf

middle: L


title: The transcriptome of Klebsiella oxytoca M5a1 during onset of nitrogen fixation

city: London

first: Martin

last: Buck

address: Imperial College Road, South Kensington

department: Life Sciences

institute: Imperial College London

summary:
Purpose: Klebsiella oxytoca M5a1 (previously Klebsiella pneumonia M5a1) is a principle model organism for free-living biological nitrogen fixation. This strain has been used for decades in the characterisation of nitrogenase function and the genetic regulation of nitrogen fixation physiology. Currently it represents a key model for synthetic biology and biotechnology approaches. This project involves a multi-omics approach to modelling nitrogen physiology in Klebsiella oxytoca M5a1, in order to inform rational genetic engineering for improved nitrogen fixation activity. Here we studied the transition from nitrogen replete (high NH4Cl) to nitrogen starved (NH4Cl run-out) conditions, the latter of which induce nif gene expression and synthesis of the nitrogenase enzyme. We mapped RNA-sequencing (Illumina) reads to our assembled M5aI genome in order to compare the transcriptome between nitrogen replete and nitrogen fixing conditions using differential gene expression (DEG) analysis.
Methods: Total RNA was extracted from fixed M5a1 cell samples after culturing in nitrogen replete (10 mM NH4Cl; one replicate) or nitrogen starved (3 hours after complete run-out of 0.5 mM NH4Cl; two replicates) growth medium (NFDM). cDNA libraries were prepared for Illumina (NextSeq 500) sequencing, with a read length of 75 nt and a depth of 100 million reads. Following processing and quality control, sequence reads were mapped to a M5a1 genomic template (GenBank WGS accession JAFHKG010000000; BioSample SAMN17288411) and gene count normalisation performed (RPKM). Differential gene expression analysis was performed using the DEseq2 package utilising settings of regularized logarithm (rlog) normalisation of read counts, Wald hypothesis testing and p-value adjustment using a False Discovery Rate threshold of 0.05. Log2 fold changes between conditions were calculated for differentially expressed genes (DEGs) with an adjusted p value of <0.05.
Results: Across the three samples, between 22.0-25.1 million reads (81.4-87.7%) were mapped to the genome, including 56.7-68.5% mapped to annotated genes. More than 50% of genes (2694/5279 genes) were differentially expressed (adjusted p-value <0.05) in the nitrogen starved condition with respect to the nitrogen replate condition. 925 genes were upregulated and 1117 genes downregulated by more than 2-fold. Of these, 1515 differentially expressed genes correspond to annotated proteins in the KEGG functional orthology (KO) database. The 20 nitrogen fixation (nif) genes were ranked among the 200 genes with highest calculated expression values (RPKM) in the nitrogen starved condition.
Conclusions: Our study provides a detailed insight into the global gene expression profile associated with diazotrophic (nitrogen fixing) growth, revealing a dominant role for nif and other nitrogen regulatory genes in the adaptation to nitrogen stress, in addition to a large array of secondary genes indirectly associated with shifts in metabolism and growth phenotype (e.g. metabolic enzymes, gene expression machinery, transporters).

overall_design: Examination of wild-type M5a1 transcriptome in nitrogen starved growth medium (2 biological replicates) with respect to nitrogen replete control (1 replicate)

first: Christopher

middle: J

last: Waite

first: Jorg

last: Schumacher


title: Transcriptional regulation of miR-30a by YAP impacts PTPN13 and KLF9 levels and Schwann cell proliferation

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

summary: The Hippo pathway is a key regulatory pathway that is tightly regulated by mechanical cues such as tension, pressure and contact with the extracellular matrix and other cells. At the distal end of the pathway is the Yes-associated protein (YAP), a well-characterized transcriptional regulator. Through binding to transcription factors (TFs) such as the TEA-Domain TFs (TEADs) YAP regulates expression of several genes involved in cell fate, proliferation and death decisions. While the function of YAP as direct transcriptional regulator has been extensively characterized, only a small number of studies examined YAP function as a regulator of gene expression via microRNAs. We utilized bioinformatic approaches, including ChIP-seq and RNA-seq, to identify potential new targets of YAP regulation and identified miR-30a as a YAP target gene in Schwann cells.  We find that YAP binds to the promoter and regulates the expression of miR-30a. Moreover, we identify several YAP-regulated genes that are putative  miR-30a targets and focus on two of these, PTPN13 and KLF9. We find that YAP regulation of Schwann cell proliferation is mediated, to a significant extent, through miR-30a regulation of PTPN13 in Schwann cells. These findings identify a new regulatory function by YAP, mediated by miR-30a, to downregulate expression of PTPN13, and KLF9. These studies expand our understanding of YAP function as a regulator of miRNAs and illustrate the complexity of YAP transcriptional functions.

overall_design: 4 samples, 3 replicates each

first: Joseph

last: Kissil

first: Alyssa

last: Shepard

first: Sany

last: Hoxha

middle: S


title: The role of histone variant H3.3 regulation by HIRA in hematopoiesis

status: Public on Jul 08 2021

city: Houston

first: Rebecca

last: Murdaugh

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine


title: The role of histone variant H3.3 regulation by HIRA in hematopoiesis (RNA-seq)

summary: Histone variants contribute to the complexity of the chromatin landscape and play an integral role in defining DNA domains and regulating gene expression. The histone H3 variant H3.3 is incorporated into genic elements independent of DNA replication by its chaperone HIRA. Here we demonstrate that Hira is required for the self-renewal of adult hematopoietic stem cells (HSCs) and to restrain erythroid differentiation. Deletion of Hira led to rapid depletion of HSCs while differentiated hematopoietic cells remained largely unaffected. Depletion of HSCs after Hira deletion was accompanied by increased expression of bivalent and erythroid genes, which were exacerbated upon cell division and paralleled increased erythroid differentiation. Assessing H3.3 occupancy identified a subset of polycomb-repressed chromatin in HSCs that depend on HIRA to maintain the inaccessible, H3.3-occupied state for gene repression. HIRA-dependent H3.3 incorporation thus defines distinct repressive chromatin that represses erythroid differentiation of HSCs.

overall_design: RNA-seq in WT and HIRA KO HSCs and MPPs sorted from adult bone marrow with 4 biological replicates each, and RNA-seq in WT and HIRA KO HSCs and MPPs that are H2B-GFP High or H2B-GFP Low sorted from adult bone marrow with 3 biological replicates each.

first: Kevin

last: Hoegenauer

first: Daisuke

last: Nakada


title: sequential DNA affinity purification sequencing (seq-DAP-seq) data of SEP3-AGAPI

city: Grenoble

first: Romain

last: BLANC-MATHIEU

address: 17 Avenue des martyrs

country: France

institute: CEA

summary: In this study, we applied sequential DNA affinity purification sequencing (seq-DAP-seq) to identiy genome-wide binding of a heterocomplex formed by two transcription factors of the MADS familly SEP3 and AG(AP1-I) (AG with its I domain switched with that of AP1). We compared the genome wide binding of SEP3-AG(AP1-I) to that of our previously published SEP3-AG data

first: Xuelei

last: Lai

last: Blanc-Mathieu

first: Jérémy

last: Lucas

first: Véronique

last: Hugouvieux

first: François

last: Parcy

first: Chloe

last: Zubieta


title: Expression of RUNX1-JAK2 in Human Induced Pluripotent Stem Cell-Derived Hematopoietic Cells Activates the JAK-STAT and MYC Pathways.

city: Vienna

first: Klaus

middle: Josef

last: Fortschegger

state: Austria

address: Zimmermannplatz 10

department: Genetics of Leukemia

country: Austria

institute: St. Anna Kinderkrebsforschung

summary: A heterogeneous genetic subtype of B-cell precursor acute lymphoblastic leukemia is driven by constitutive kinase-activation, including patients with JAK2 fusions. In our study, we model the impact of a novel JAK2 fusion protein on hematopoietic development in human induced pluripotent stem cells (hiPSCs). We insert the RUNX1-JAK2 fusion into one endogenous RUNX1 allele through employing in trans paired nicking genome editing. Tagging of the fusion with a degron facilitates protein depletion using the heterobifunctional compound dTAG-13. Throughout in vitro hematopoietic differentiation, the expression of RUNX1-JAK2 is driven by endogenous RUNX1 regulatory elements at physiological levels. Functional analysis reveals that RUNX1-JAK2 knock-in cell lines yield fewer hematopoietic progenitors, due to RUNX1 haploinsufficiency. Nevertheless, these progenitors further differen-tiate toward myeloid lineages to a similar extent as wild-type cells. The expression of the RUNX1-JAK2 fusion protein only elicits subtle effects on myeloid differentiation, and is unable to transform early hematopoietic progenitors. However, phosphoprotein and transcriptome analyses reveal that RUNX1-JAK2 constitutively activates JAK-STAT signaling in differentiating hiPSCs and at the same time upregulates MYC targets—confirming the interaction between these pathways. This proof-of-principle study indicates that conditional expression of oncogenic fusion proteins in combination with hematopoietic differentiation of hiPSCs may be applicable to leukemia-relevant disease modeling.

overall_design: Differential gene expression analysis using RNA-seq of three wild-type controls (WT) and six RUNX1-JAK2 clones (RJ), each either dTAG-13-treated or not.

first: Anna-Maria

last: Husa

first: Dagmar

last: Schinnerl

first: Karin

last: Nebral

first: Sabine

last: Strehl


title: The regulatory impact of RNA-binding proteins on microRNA targeting

city: Seoul

first: Daehyun

last: Baek

address: Rm 402, Bldg 504, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: Argonaute is the primary mediator of metazoan miRNA targeting (MT). Among the currently identified >1,500 human RNA-binding proteins (RBPs), there are only a handful of RBPs known to enhance MT and several others reported to suppress MT, leaving the global impact of RBPs on MT elusive. In this study, we have systematically analyzed transcriptome-wide binding sites for 150 human RBPs and evaluated the quantitative effect of individual RBPs on MT efficacy. In contrast to previous studies, we show that most RBPs significantly affect MT and that all of those MT-regulating RBPs function as MT enhancers rather than suppressors, by making the local secondary structure of the target site accessible to Argonaute. Our findings illuminate the unappreciated regulatory impact of human RBPs on MT, and as these RBPs may play key roles in the gene regulatory network governed by metazoan miRNAs, MT should be understood in the context of co-regulating RBPs.

overall_design: mRNA-seq and sRNA-seq expression profiles and whole-transcriptome response to ectopically introduced or deleted miRNAs in human cell lines

first: Sukjun

last: Kim


title: Distinct signaling pathways distinguish in vivo from in vitro growth in murine ovarian follicle activation and maturation

status: Public on Jul 07 2021

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

institute: Omiics ApS

summary: We record the application of RNA sequencing of murine ovarian follicles and mature oocytes during inv itro and in vivo growth.

overall_design: Differential gene expression comparison

first: Mahboobeh

last: Amoushahi

last: Lykke-Hartmann


title: The role of histone variant H3.3 regulation by HIRA in hematopoiesis (ATAC-Seq)

first: Rebecca

last: Murdaugh

overall_design: ATAC-seq in WT and HIRA KO HSCs sorted from adult bone marrow with 3 biological replicates each.

first: Kevin

middle: A

last: Hoegenauer

first: Matthew

middle: C

last: Hill

last: Nakada


title: Enhancer decommissioning during inner ear maturation imposes an epigenetic barrier to sensory hair cell regeneration

city: Los Angeles

first: Neil

last: Segil

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

summary: Latent transdifferentiation potential exists in supporting cells at neonatal stage in the organ of Corti in mouse, but this plasticity is lost rapidly during the first week of postnatal maturation, leading to the failure of sensory hair cell regeneration. To investigate the molecular mechanism underlying the loss of transdifferentiation potential, we compared epigenetic changes in E17.5, P1 and P6 supporting cells. In E17.5 and P1 supporting cells, hair cell gene enhancers are kept in a primed state (H3K4me1+ H3K27ac-) which can be readily activated during transdifferentiation induced by Notch blocking. As supporting cells mature, a substantial amount of hair cell gene enhancers are decommissioned by H3K4me1, leading to the loss of transdifferentiation potential. In contrast, hair cell gene enhancers retain their commissioned epigenetic status in mature utricular supporting cells, sustaining the transidifferentiation potential in utricular supporting cells in mature animals. Our findings reveal the epigenetic mechanisms underlying the failure of sensory hair cell regeneration in mammalian cochlea.

overall_design: P1 cochlear sensory hair cells (Atoh1-GFP+) were FACS purified for transcriptome and epigenetic profiling to hair cell gene identification and enhancer prediction. E17.5, P1 and P6 supporting cells (Lfng-GFP+) were collected for transcriptomic and epigenetic analyses to survey the epigenetic changes surrounding hair cell gene elements. Activation of hair cell gene elements was interrogated by comparing epigenetic profiles between transdifferentiating supporting cells (permissive; Lfng-CreER/TdTomato+ Atoh1-GFP+) and non-transdifferentiating supporting cells (non-permissive; Lfng-CreER/TdTomato+). In addition, P21 utricular supporting cells (Lfng-GFP+) were compared to their cochlear counterpart.


title: Chromatin Interaction Neural Network (ChINN): A machine learning-based method for predicting chromatin interactions from DNA sequences

city: Singapore

first: Melissa

last: Fullwood

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

summary: Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. Various computational methods have been developed to predict chromatin interactions. Most of these methods rely on large collections of ChIP-Seq/RNA-Seq/DNase-Seq datasets and predict only enhancer-promoter interactions. Some of the ‘state-of-the-art’ methods have poor experimental designs, leading to over-exaggerated performances and misleading conclusions. Here we developed a computational method, Chromatin Interaction Neural Network (CHINN), to predict chromatin interactions between open chromatin regions by using only DNA sequences of the interacting open chromatin regions. CHINN is able to predict CTCF-, RNA polymerase II- and HiC-associated chromatin interactions between open chromatin regions. CHINN also shows good across-sample performances and captures various sequence features that are predictive of chromatin interactions. We applied CHINN to 90 chronic lymphocytic leukemia (CLL) samples and detected systematic differences in the chromatin interactome between IGVH-mutated and IGVH-unmutated CLL samples.

overall_design: We generated Hi-C, ATAC-seq, and RNA-seq libraries for 6 CLL samples. Chronic Lymphocytic Leukemia patient samples (either peripheral blood or bone marrow isolates) were obtained from the Leukemia Cell Bank at the National University Health System (NUHS) with patient consent, under Institute Review Board number H-20-022E. The CLL samples were either bone marrow aspirates (312,324,344,484, and 102) or peripheral blood (401).

first: Fan

last: Cao

first: Yu

last: Zhang

first: Yichao

last: Cai

first: Sambhavi

last: Animesh

first: Ying

first: Semih

last: Akincilar

first: Yan Ping

last: Loh

first: Xinya

last: Li

first: Wee-Joo

last: Chng

first: Vinay

last: Tergoankar

first: Chee Keong

last: Kwoh


title: MAIT cells regulate NK cell mediated tumor immunity (NanoString)

status: Public on Jul 06 2021

city: Melbourne

first: Paul

last: Beavis

state: Victoria

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: This study reveals the dichotomous role of MAIT cells in regulating NK cell mediated anti-tumor immunity.

overall_design: B6-MAITcast MR1 WT mice were treated intranasally with 50ul PBS or 233uM 5-OP-RU on days 0, 1, 2 and 4. Day 6 lungs were harvested and RNA was extracted using RNAeasy (Qiagen) kit as per manufacturers instructions

first: Emma

last: Petley

last: Sek


title: Transcriptional profiling of human fibroblasts cells from normal, PD patient, and PD patient treatment with mouse cavernous pericyte-derived extracellular vesicles-mimetic nanovesicles (PC-NVs)

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

institute: Inha university hospital

summary: Peyronie’s disease (PD) is a severe fibrotic diseases in the tunica albuginea that causes penis curvatures and leads to penile pain, deformity as well as erectile dysfunction (ED). The role of pericytes in the pathogenesis of fibrosis have been perceived recently. Extracellular vesicles (EVs)-mimetic nanovesicles (NVs) have emerged particular interest in intercellular communication between cells in various fields of fibrosis disease. However, the global gene expression of pericytes-derived EVs-mimetic NVs in regulating fibrosis remains unknown. Here we used RNA-sequencing technology to investigate the potential target genes regulated by pericytes-derived EVs-mimetic NVs in primary fibroblasts derived from human PD plaque.

overall_design: human normal fibroblasts (NF, n=4), human PD fibroblasts (PF, n=4) and human PD fibroblasts treatment with PC-NVs (PFPC, N=4)

first: Guo

middle: N

last: Yin

first: Shuguang

last: Piao

first: Ji-Kan

last: Ryu

first: Jun-Kyu

last: Suh


title: Deep learning detects cardiotoxicity in a high-content screen with induced pluripotent stem cell-derived cardiomyocytes

city: South San Francisco

first: Farshad

last: Farshidfar

address: 171 Oyster Point Blvd Ste 500

country: USA

institute: Tenaya Therapeutics Inc.

summary: Drug-induced cardiotoxicity and hepatotoxicity are major causes of drug attrition. To decrease late-stage drug attrition, pharmaceutical and biotechnology industries need to establish biologically relevant models that use phenotypic screening to detect drug-induced toxicity in vitro. In this study, we sought to rapidly detect patterns of cardiotoxicity using high-content image analysis with deep learning and induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). We screened a library of 1280 bioactive compounds and identified those with potential cardiotoxic liabilities in iPSC-CMs using a single-parameter score based on deep learning. Compounds demonstrating cardiotoxicity in iPSC-CMs included DNA intercalators, ion channel blockers, epidermal growth factor receptor, cyclin-dependent kinase, and multi-kinase inhibitors. We also screened a diverse library of molecules with unknown targets and identified chemical frameworks that show cardiotoxic signal in iPSC-CMs. By using this screening approach during target discovery and lead optimization, we can de-risk early-stage drug discovery. We show that the broad applicability of combining deep learning with iPSC technology is an effective way to interrogate cellular phenotypes and identify drugs that may protect against diseased phenotypes and deleterious mutations.

overall_design: RNA sequencing on samples treated with our previously selected 9 cardiotoxic drugs (2 replicates/drug) and DMSO-treated iPSC-CMs (6 replicates).

first: Francis

last: Grafton

first: Jaclyn

last: Ho

first: Sara

last: Ranjbarvaziri

first: Ana

last: Budan

first: Stephanie

last: Steltzer

first: Mahnaz

last: Maddah

first: Kevin

last: Loewke

first: Kristina

last: Green

first: Snahel

last: Patel

first: Tim

last: Hoey

first: Mohammad

last: Mandegar


title: MAIT cells regulate NK cell mediated tumor immunity (RNA-Seq)

first: Paul

last: Beavis

overall_design: B6-MAITcast MR1 WT mice were treated intranasally with 50ul PBS or 233uM 5-OP-RU on days 0, 1, 2 and 4. Day 6 lungs were harvested and MAIT cells and NK cells were sorted via FACS and RNA was extracted using RNAeasy (Qiagen) kit as per manufacturers instructions

first: Emma

last: Petley

last: Sek


title: The role of histone variant H3.3 regulation by HIRA in hematopoiesis (ChIP-Seq)

first: Rebecca

last: Murdaugh

overall_design: ChIP-seq for endogenous histone variant H3.3 in WT and HIRA KO HSCs from adult bone marrow sorted 7 days after treating mice with a low dose of pIpC to induce HIRA KO, 2 biological replicates for each IP sample, 1 replicate for each input sample

last: Hoegenauer

first: Daisuke

last: Nakada


title: The WDR5-H3K4me3 epigenetic axis regulates OPN expression to compensate PD-L1 function to promote pancreatic cancer immune escape [ChIP-seq]

first: Huidong

last: Shi

summary: Total RNA was isolated from normal C57BL/6 mouse pancreas, PANC02-H7, and UN-KC-6141 tumors from tumor-bearing mice. The RNA was used for RNA-Seq. The gene expression profiles between normal mouse pancreas and orthotopic pancreatic tumors were compared, and differentially expressed genes were identified.

overall_design: Normal mouse pancreas and tumors from tumor-bearing mice were used for chromatin fragment preparation. Anti-H3K4me3 antibody was used for ChIP, followed by library construction and ChIP-sequencing. The genome-wide H3K4me3  profiles between normal mouse pancreas and orthotopic pancreatic tumors were compared. Genes with differential H3K4me3 depositions at their promoter regions were identified.

first: Chunwan

last: Wu

first: Kebin

last: Liu


title: N-linked glycoproteins from exosome-depleted excretory-secretory products of fourth-stage larval Angiostrongylus cantonensis promotes alternative activation of macrophages through metabolic reprogramming by the PI3K-Akt pathway

status: Public on Jul 05 2021

first: Xi

last: Sun

state: Guangdong

address: Zhongshan 2nd road

department: Department of parasitology

institute: Sun yat-sen university

summary: In this study, Angiostrongylus cantonensis (AC), which parasitizes in the brain of the non-permissive host, such as mouse and human, is an etiologic agent of eosinophilic meningitis. Excretory-secretory (ES) products play an important role in the interaction between parasites and hosts’ immune responses. Inflammatory macrophages are responsible for eosinophilic meningitis induced by AC, and the soluble antigens of Angiostrongylus cantonensis fourth stage larva (AC L4), a mimic of dead AC L4, aggravate eosinophilic meningitis in AC-infected mice model via promoting alternative activation of macrophages. While whether AC L4 ES products, as well as its exosome-depleted excretory-secretory products (exofree) component play a role on macrophage activation remains unknown. In order to identify the AC L4 exofree signature regulating genes, BMDMs were treated with PBS (ctr), free (AC L4 exofree), IL-4, com (IL-4+AC L4 exofree) for 6h, 12h, and 24 h respectively and RNA-seq analysis was performed.

overall_design: mRNA profiles of BMDMs treated with PBS (ctr), free (AC L4 exofree), IL-4, com (IL-4+AC L4 exofree) for 6h, 12h, and 24 h

first: Shuo

last: Wan

first: Xiaoqiang

first: Wenyan

last: Tang

first: Lifu

last: Wang

first: Zhongdao


title: Single cell analysis of CD4 T cells and an ILCs  in nasal polyps

status: Public on Jul 02 2021

city: Solna

first: Christopher

last: Tibbitt

state: Stockholms län

address: C7 Biomedicum

department: MTC

institute: Karolinksa Institutet

summary: Chronic rhinosinusitis with nasal polyps (CRSwNP) is characterized by a chronic inflammatory   process often associated with comorbid asthma. In this study, we analysed the transcriptomes   of single T helper (Th) cells from nasal polyps of patients with CRS and validated these   findings using multiparameter flow cytometry. Polyp tissue contained suppressive Treg and   Th2 cells, type 2 innate lymphoid cells (ILC2) and 3 transcriptionally distinct subsets of   cytotoxic CD4 T cells (CD4 CTL). GATA3 expression was a feature of polyp Treg while Th2   cells highly expressed TCN1, CD200R, HPGDS and were enriched for genes involved in lipid   metabolism. Only a portion of polyp Th2 cells expressed the prostaglandin D2 receptor   CRTH2, while a subpopulation of CD109+CRTH2- Th2 cells expressed mRNA for common   inhibitor receptors and produced IL-10. Taken together, we resolve the complexity of T helper   cells in CRSwNP patients to identify several distinct clusters of CD4 CTL and a population of   CD109+CRTH2- Th2 cells with putative regulatory potential.

overall_design:
Herein, we performed  scRNA-Seq of CD4 T cells and functionally related innate lymphoid cells  (ILC) in nasal polyp tissue, with a view to defining the functional heterogeneity of these cells in CRSwNP patients. Viable Th cells (CD4+ CD3+ CD20- CD14- ) and ILC2 (CD4- CD3- CD20- CD14- CRTH2+ ) were sorted using an Aria FUSION sorter using FACS DIVA software (BD Biosciences). Cells were then washed in cold PBS prior to loading on the droplet-based Chromium microfluidic system (10X Genomics). Paired gene expression and TCR libraries were prepared using the 5’ v1 10X Genomics kit.
-------------------------
>>>Submitter declares that the raw data for samples will be deposited in EGA due to patient privacy concerns.<<<

first: Chris

first: Jonathan

last: Coquet


title: Decreased piRNAs in infertile semen are related to downregulation of sperm MitoPLD expression

city: Hangzhou

first: yanqian

last: wu

address: 8 Yikang Road, Lin’an District, Hangzhou, Zhejiang, P.R.China

institute: hangzhou medical college

type: Non-coding RNA profiling by high throughput sequencing

summary: Currently, the molecular mechanisms for the cause of male infertility are still poorly understood. Our previous study has demonstrated that PIWI-interacting RNAs (piRNAs) are downregulated in seminal plasma of infertile patients and can serve as molecular biomarkers for male infertility. However, the source and mechanism for the dysregulation of piRNAs remain obscure. In this study, we found that exosomes are present in high concentrations in human seminal plasma and confirmed that piRNAs are predominantly present in the exosomal fraction of seminal plasma. Moreover, we showed that piRNAs were significantly decreased in exosomes of asthenozoospermia patients compared with the fertile controls. By systematically screening piRNA profiles in sperms of fertile controls and asthenozoospermia patients, we found that piRNAs were parallelly reduced during infertility. At last, we investigated the expression of proteins that are essential for piRNAs biogenesis in sperms and therefore identified a tight correlation between the levels of spermatozoa piRNA and MitoPLD protein, suggesting that the loss-of-function of MitoPLD could cause a severe defect of piRNA accumulation in sperms. In summary, this study identified a parallel reduction of piRNAs and MitoPLD protein in sperms of infertile patients, which may provide pathophysiological clues about the development of infertility.

overall_design: Fresh samples were collected and stored at -80℃.Total RNA of sperm were extracted and high-throughput sequencing was performed.

first: Yeting

last: Hong

first: Yanqian


title: Identification of Genes and miRNAs Affecting Pre-harvest Sprouting in Rice (Oryza sativa L.) by Transcriptome and Small RNAome Analyses

status: Public on Jul 04 2021

city: SEOUL

first: Chanseok

last: Shin

address: Gwanak-gu Daehak-dong

summary:
Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages in rice seed embryo with profile of miRNA-seq.
Methods: Oryza sativa. L miRNA profiles of two different ecotypes with 3 different maturation stages of rice seed embryo were generated by NGS, in duplicate, following Illumina NGS workflow.
Results: We found the differentially expressed microRNAs between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. Target transcripts of differentially expressed microRNAs have been predicted via psRNATarget web server, and a part of those target genes are likely to be regulated by microRNAs, affecting overall responses to heat stress and the regulation of seed dormancy during maturation.
Conclusions: Our study represents the analysis of rice seed small RNAs, specifically microRNAs, under two different ecotypes, three different seed maturation stages in rice seed embryo. Our results show that microRNAs are involved in response to heat stress and the regulation of seed dormancy. This study will provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.

overall_design: smRNA profiles from embryo of two different rice (Oryza sativa L.) ecotypes

first: Minsu

last: Park

first: Woochang

last: Choi

first: Sang-Yoon

first: Hongman

last: Moon

first: Dowhan

last: Lee

first: Yun-Shil

last: Gho

first: Ki-Hong

last: Jung

first: Jong-Seong

last: Jeon


title: High throughput screening identifies microRNAs regulating PCSK9 and LDL receptor expression

city: New York City

first: Coen

last: van Solingen

state: New York

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

summary: Using a high throughput human microRNA library screen, we identified microRNAs targeting the 3’untranslated region of human PCSK9

overall_design: The high throughput human miRNA screen was conducted with the NYU RNAi Core using a human microRNA library from Ambion mirVana, Life Technologies. HEK293T cells were seeded in a 384-well, white solid bottom polystyrene TC-treated microplates and co-transfected with 1.5 pmol of miRNA mimic, and 10 ng of total DNA plasmids composed of a 2:1 ratio of PCSK9 3’-UTR firefly luciferase reporter plasmid (Switchgear Genomics) to renilla luciferase control plasmid using Lipofectamine 2000 (Invitrogen). The cells and transfection mix and were dispensed into the 384-well plates using a Wellmate/BioTek Dispenser (ThermoScientific) outfitted with small-bore tubing. The plates were centrifuged at 1,000x g for 1 min to settle the contents and then incubated in a humidified incubator at 37°C and 5% CO2 for 48 hours. To measure PCSK9 3’UTR-luciferase activity, media was aspirated and the wells were washed with 1xPBS using a EL406 Microplate Washer (BioTek). Luciferase activity was assayed with the Dual-Glo Luciferase Assay® (Promega) according to the manufacturer’s instructions and read on a spectrophotometer (Envision). Positive (miR-224) and negative control miRNAs were included on each screen plate, and the miRNA library was assayed in quadruplicate. PCSK9 3’UTR firefly luciferase values were normalized to those of control renilla luciferase values for each replicate.

first: Kathryn

last: Moore


title: Diet-induced alteration of intestinal stem cell function underlies obesity and pre-diabetes in mice

city: Neuherberg

first: Sophie

last: Tritschler

address: Ingolstädter Landstrasse 1

institute: Helmholtz Zentrum Munich

summary: This dataset consists of single-cell RNA-seq (10X) data from small intestinal crypts of healthy and HFHSD induced obese mice Foxa2-FVF/FVF mice and from small intestinal villi of healthy and HFHSD induced obese C57BL/6N mice. Mice were fed a HFHSD for 12 weeks. Intestinal crypt cell samples were FVF-enriched with FVF+ cells in a 1:1 ratio (50% FVF+, 50% FVF-) before sequencing.

overall_design: Single cell RNA seq experiments of isolated small intestinal cryptes and villi from adult mice were performed using 10X Genomics technology to generate single cell transcriptomic profiles of healthy and high-fat-high-sugar-diet (HFHSD) induced obese mice.

first: Alexandra

last: Aliluev

first: Michael

last: Sterr

first: Lena

last: Oppenländer

first: Julia

last: Hinterdobler

first: Greisle

last: Tobias

first: Martin

last: Irmler

first: Johannes

last: Beckers

last: Sun

first: Axel

last: Walch

first: Kerstin

last: Stemmer

first: Alida

last: Kindt

first: Jan

last: Krumsiek

first: Matthias

middle: H

last: Tschöp

first: Fabian

last: Theis

first: Heiko

last: Lickert

first: Anika

last: Böttcher


title: Development of quantitative direct prediction algorithm for the human target organ similarity of human pluripotent stem cell-derived organoids and cells [scRNA-seq]

city: Daejeon

first: Jaeeun

last: Jung

address: 125 Gwahak-ro, Youseong-gu

institute: KRIBB

summary: We constructed aquantitative calculation system (organ-specific panels and calculation algorithm) to assess thesimilarity to the human lung, stomach, and heart and confirmed the algorithm using in-houseRNA-seq data (total RNA from 20 tissues). To evaluate our system, we generated hPSC-derived lung organoids, gastric organoids, and cardiomyocytes and detected 33.4%, 51.7%, and 83.4% similarity, respectively, to the corresponding human target organs.

overall_design: Human organ similarity calculation system for hPSC derived organoid and cell based on RNA-seq analysis.

first: Hyun-Soo

last: Cho

first: Dae-Soo

last: Kim

first: Mi-Young

last: Son


title: Development of quantitative direct prediction algorithm for the human target organ similarity of human pluripotent stem cell-derived organoids and cells [RNA-seq]


title: Single-cell transcriptomic profiling reveals distinct mechanical responses between normal and diseased tendon progenitor cells

city: Stanford

first: Christopher

last: Still

state: California

address: 443 Via Ortega, Room 376

institute: Stanford

summary: Regenerative medicine approaches utilizing stem cells offer a promising strategy to address tendinopathy, a class of common tendon disorders associated with pain and impaired function. Tendon progenitor cells (TPCs) are important in healing and maintaining tendon tissues. Here we provide a comprehensive single cell transcriptomic profiling of TPCs from three normal and three clinically classified tendinopathy samples in response to mechanical stimuli. Analysis reveals seven distinct TPC subpopulations including subsets that are responsive to the mechanical stress, highly clonogenic, and specialized in cytokine or growth factor expression. The single cell transcriptomic profiling of TPCs and their subsets serves as a foundation for further investigation into the pathology and molecular hallmarks of tendinopathy in mechanical stimulation conditions.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: scRNAseq of human TPCs from normal and diseased patellar tendon.

first: Chris

last: Still II

first: Wen-Teh

last: Chang

first: Seth

last: Sherman

first: Kyle

middle: R

last: Sochacki

first: Jason

last: Dragoo

first: Lei

last: Qi


title: Development of quantitative direct prediction algorithm for the human target organ similarity of human pluripotent stem cell-derived organoids and cells

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: A novel mouse stem cell established in combination of Activin A and LIF

city: Hohhut

first: Mengyi

last: Wei

state: Inner Mongolia

address: Zhao Jun Road No.24

department: Life Science department

institute: Inner Mongolia University

summary: We reported the ALSCs derivation from E3.5 blastocysts and E6.5 epiblasts cultured in basic N2B27 medium supplemented with Acitivin A and LIF. Activin A subtitutes NODAL signaling in vivo and is an important factor for self-renewal. LIF is extracted from feeder and have an impact on sustaining pluripotency of ESCs. We combined the two factors and finding AL medium could sustaining a novel mouse embryonic stem cells. Furthermore, EpiSCs are also discovered that able to convert to rESCs by culturing in AL medium for several passages, which illustrates that AL medium not only support establishment of pluripotent stem cells from embryos in vivo but also could convert EpiSCs to rESCs. Then, based on multiple analyses of pluripotency, we performed RNA-seq of ALSCs to exploring the differences of ALSCs compared to EpiSCs and ESCs respctively. RNA-seq data showed ALSCs is different with EpiSCs or ESCs. Teratoma test proved ALSCs could contribute to three germ layers in vivo and embryonic body analysis testify ALSCs could differentiate to three germ layers like cells in vitro.

overall_design: 3 replicates of mRNA of ALSCs. The control group named AFSCs and have been submitted in GSE130060.

first: Yanglin

last: Chen


title: Gene expression associated with acquired paclitaxel resistance in ovarian cancer cell lines

city: Lexington

first: Joseph

middle: Robert

last: McCorkle

state: KY

address: 760 Press Ave.

institute: University of Kentucky

summary: Conventional frontline treatment for ovarian cancer consists of successive chemotherapy cycles of paclitaxel and platinum. Despite the initial favorable responses for most patients, chemotherapy resistance frequently leads to recurrent or refractory disease. New treatment strategies that circumvent or prevent mechanisms of resistance are needed to improve ovarian cancer therapy. We developed in vitro ovarian cancer cell line models of acquired paclitaxel resistance using 2 immortalized human ovarian cancer cell lines, OVCAR3 and TOV-21G. We also developed in vitro primary ovarian cancer organoid models using tumor tissue from 7 patients with gynecologic malignancies. Gene expression differences in resistant and sensitive lines were analyzed by RNA sequencing to identify potential mechanisms of paclitaxel resistance in primary ovarian cancer.

overall_design: Paclitaxel-resistant and parental control cells derived from 2 distinct ovarian cancer cell lines, each analyzed in triplicate (12 total samples). Paclitaxel-resistant (n=3) and sensitive (n=4) organoids derived from 7 primary ovarian tumor tissue samples

first: J

first: Jill

last: Kolesar

first: Jinpeng

last: Liu

first: Chi

last: Wang


title: RNA-seq and ATAC-seq profiling of terminal end buds and ducts from mouse mammary glands

status: Public on Jul 03 2021

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary:
The mammary glands of adult female mice were divided into ductal tissue and terminal end buds (TEBs). Basal and luminal epithelial cells were FACS sorted. RNA and nuclei were extracted for RNA-seq and ATAC-seq profiling using an Illumina NextSeq 500 sequencer.
This SuperSeries is composed of the SubSeries listed below.

overall_design:
Tissue was extracted from three independent mouse pools resulting in n=3 biological replicates of each cell population from each tissue.
Refer to individual Series


title: Areca catechu-(Betel-nut)-induced whole transcriptome changes in a human monocyte cell line that may have relevance to diabetes and obesity; a pilot study

status: Public on Jul 01 2021

city: London

first: Graham

last: Hitman

address: 4 Newark St

institute: Queen Mary University of London

summary: Betel-nut consumption is the fourth most common addictive habit  globally and there is good evidence linking the habit to obesity, type 2 diabetes (T2D)  and the metabolic syndrome. The aim of our pilot study was to identify gene expression  relevant to obesity, T2D and the metabolic syndrome using a genome-wide  transcriptomic approach in a human monocyte cell line incubated with arecoline and its  nitrosated products.

overall_design: 3 THP1 samples treated with Arecoline and 3 samples treated with MNPA


title: Epigenetic changes during long term intestinal organoid culture

city: Leipzig

first: Torsten

last: Thalheim

address: Härtelstr. 16 – 18

department: Interdisciplinary Centre for Bioinformatics

institute: Leipzig University

summary: Organoids retain the morphological and molecular patterns of their tissue of origin, are self-organizing, relatively simple to handle and accessible to genetic engineering. Thus, they represent an optimal tool for studying mechanisms of tissue maintenance and aging. Long-term expansion under standard growth conditions, however, is accompanied by changes in growth pattern and kinetics. As a potential explanation of these alterations, epigenetic drifts in organoid culture have been suggested. Here, we study histone tri-methylation at lysine 4 (H3K4me3) and 27 (H3K27me3) and transcriptome profiles of intestinal organoids derived from mismatch repair (MMR)-deficient and control mice and cultured for 3 and 20 weeks, and compare them with data on their tissue of origin. We find that, besides the expected changes in short-term culture, organoids show profound changes in their epigenome also during long-term culture. The most prominent are epigenetic gene activation by H3K4me3 recruitment to previously unmodified genes and by H3K27me3 loss from originally bivalent genes. We show that long-term culture is linked to broad transcriptional changes that indicate an ongoing maturation and metabolic adaptation process. This process is disturbed in MMR-deficient mice, resulting in endoplasmic reticulum (ER)-stress and Wnt-activation.  Our results can be explained in terms of a mathematical model assuming that epigenetic changes during long-term culture involve DNA de-methylation that ceases if the metabolic adaptation is disturbed.

overall_design: Examination of histone H3K4 and H3K27 modifications in 4 and 20 weeks old intestinal organoids derived from MMR-deficient and control mice.

first: Susann

last: Siebert

first: Marianne

last: Quaas

first: Maria

last: Herberg

first: Michal

last: Schweiger

first: Joerg

last: Galle

first: Gabriela

last: Aust


title: IL-33 stimulates DCs to express SEMA4A

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: We hypothesized that IL-33 created Tc1-like condition in the modifying tumor microenvironment (TME). RNA-seq analysis of dendritic cells (DCs) showed the elevation of Il1rl1 and SEMA4A by IL-33, the latter of which was confirmed by qPCR, without significant upregulation of IL-12.

overall_design: We conducted RNA sequencing on IL-33 and PBS treated CD11c+ dendritic cells in triplicate.

first: Suga

last: Yasuhiko


title: Single nucleus RNA sequence (snRNAseq) analysis of the spectrum of trophoblast lineages generated from human pluripotent stem cells in vitro

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

summary: We report the single nuclear RNA sequencing analysis for the profiling of trophoblast lineages generated from human embryoinc stem cells (hESCs) in vitro under 20 % and 5 % O2 concentration conditions. The hESCs were exposed to bone morphogenetic protein 4 (BMP4) in presence of inhibitors of  ACTIVIN/TGFB (A83–01) and FGF2 (PD1730) signaling formerly called BAP treatment for 8 days after passaging, which  generated a mixture of cytotrophoblast, syncytiotrophoblast, and HLA-G positive cells with similarities to extravillous trophoblast under both high and low O2 conditions (20 % and 5 %, respectively). A single nuclei RNA sequence approach from both O2 conditions determined two major groupings of cell clusters, one comprised of five and the second of four subcluster cell populations respectively. Of these, two  subclusters resembled extravillous trophoblast, two carried the hallmark transcripts of syncytiotrophoblast, while the remaining five were likely different kinds of mononucleated cytotrophoblast.

overall_design: Single nucleus RNA sequence (snRNAseq) analysis on Human embryonic stem cells (hESCs) converted trophoblast that are cultured under 20 % and 5 % O2 concentration conditions

first: R

last: Roberts

first: Arun

last: Seetharam

first: Teka

last: Khan


title: The Bromodomains of the mammalian SWI/SNF (mSWI/SNF) ATPases Brahma (BRM) and Brahma Related Gene 1 (BRG1) promote chromatin interaction and are critical for skeletal muscle differentiation

city: Worcester

first: Tapan

last: Sharma

state: MA

address: 368 Plantation Street

department: Gene Therapy Centre

institute: University of Massachusetts Medical School

summary: We performed RNA-seq analysis for C2C12 myoblasts as a function of differentiation. Cells were treated with either DMSO or family VIII bromodomain-specific inhibitor PFI-3 at a concentration of 50uM. We find that PFI-3 treatment affects proper differentiation of myoblasts as compared to DMSO-treated C2C12 cells. We conclude that function of mammalian SWI/SNF bromodomains is important for regulation of myoblast differentiation.

overall_design: RNA-seq data was generated from C2C12 cells induced for differentiation. Cells were treated with either DMSO or PFI-3. Samples were harvested at proliferative stage (GM) or 24h/48h post induction of differentiation (DM 24h and DM 48h). RNA from biological duplicates (for each treatment and timepoint) was extracted. Library preparation, sequencing and downstream analysis was performed by BGI Americas.

first: Anthony

last: Imbalzano


title: Transgenic MYC OFF timecourse in murine MYC-dependent cell line

city: Portland

first: Daniel

last: Liefwalker

state: Oregon

address: 2730 SW Moody Ave

department: Molecular and Medical Genetics

institute: Oregon Health and Science University

summary: In this experiment we determine MYC-dependent changes in a MYC OFF time-course.  Using the established 4188 cell line derived from the Eμ-tTA/Tet-O-MYC primary model of T-ALL, we performed RNA-seq at 0 (MYC ON), and 4, 8, 12, 24, and 48 hours after addition of 20ng/µl doxycycline (MYC OFF)

overall_design: transgenic MYC OFF timecourse in murine MYC-dependent cell line


title: Transcriptional Profiling of NASH mouse models

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

institute: University of Southern Denmark

summary: We performed RNA-seq of livers obtained from 2 different NASH mouse models

overall_design: NASH was induced in mice using two different approaches. In the first study, male C57BL/6 mice were fed with a methionine and choline deficient diet (Reseach Diet (RD): A02082002B) or a matched control low-fat diet (CD) (RD: A02082003B) for 4 weeks whereafter livers were collected for RNA-seq analyses. In a second study, male C57BL/6 mice were treated with streptozotocin at postnatal day 2 and fed with HFD from week 4 and onwards as previously described (STAM model, Fujii et al., 2013). Livers were collected at 4 weeks and 10 weeks of age followed by RNA-seq analyses.

first: Riccardo

last: Berutti

first: Stephan

last: Herzig


title: PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influence its survival in soil and rhizosphere.

city: Little Rock

first: Zulema

last: Udaondo

state: AR

address: 501 Jack Stephens Drive

department: Biomedical Informatics

institute: UAMS

summary: In this work we describe the role of paht gene from Novosphingobium sp. HR1a, as a regulator that seems to be involved in the control over the utilization of carbon and sulfur sources mainly involved in the control of pyruvate production and in the acetyl-CoA biosynthesis and PEP recycling from pyruvate.

overall_design: Examination of the level of expression of genes involved in central metabolism when pahT gene is deleted from HR1a genome and using different carbon sources.

first: Ana

last: Segura

first: Lazaro

last: Molina


title: Transcriptional Profiling of NASH mice with hepatocyte-specific knock down of Elf3 or Glis2

summary: We performed RNA-seq of livers obtained from mice fed either a control or the NASH-inducing FPC diet (Wang et al., 2016) for 24wk. In some FPC-fed mice the NASH-activated transcription factors, Elf3 or Glis2, had been deleted specifically in hepatocytes, when mice reached a steatotic state.

overall_design: HEP-INTACT mice were fed either the FPC diet or a control diet for 14wks. Mice were tail-vein injected with either AAV2/8-LP1-GFPmut-miRNA_NC, AAV2/8-LP1-GFPmut-miRNA_Elf3 or AAV2/8-LP1-GFPmut-miRNA_Glis2 (5*1011 p.f.u./mouse) and mice were kept additionally 10wks on the diet before livers were harvested for RNA-seq analyses.


title: Cell Type-Resolved Transcriptional Profiling of NASH and liver fibrosis

summary: We generated hepatocyte-specific profiles of the transcriptional landscapes during NASH progression using the INTACT methodology.

overall_design: We fed male HEP-INTACT mice two different NASH-inducing diets, 20 weeks of a FPC diet (Wang et al., 2016) or 7 weeks of a CDAHFD (Matsumoto et al., 2013), and control mice were fed a low fat diet for the same periods. Mice that had been fed NASH-inducing diets were divided into two groups, a mild and advanced NASH group, based on the liver histology. Whereas both groups had high levels of steatosis and inflammation compared to the control group, only the advanced NASH group displayed a significant degree of liver fibrosis. Livers were subsequently subjected to INTACT followed by RNA-seq analyses.


title: Comparative analysis of gene expression of cell line DU145 grown under sphere forming condition and as monolayer

city: Dresden

first: Vasyl

last: Lukiyanchuk

address: Handelallee 26

institute: OncoRay

summary: By employing a global gene expression profiling, we performed analysis of the molecular pathways which are deregulated in prostate cancer cell line DU145 grown under tumorsphere forming condition and as standard attached monolayer culture. Both oriignal DU145 and its radioresistant derivative DU145-RR were analyzed

overall_design: Tumorspheres and standart monolayer culture were compared, both for original DU145 cell line and for its radioresistant derivative DU145-RR sub-line. Each of 4 samples has been prepared in 3 repeats

first: Anna

last: Dubrovska

first: Claudia

last: Peitzsch


title: Vascepa alters expression of hepatic genes in a mouse prediabetic model.

status: Public on Jun 30 2021

city: Toronto

first: Dana

last: Al Rijjal

address: Department of Physiology, Medical Sciences Building, Room 3352, University of Toronto, 1 King's College Circle

country: Canada

institute: University of Toronto

summary:
Vascepa protects from diet induced glucose intolerance and insulin resistance in mice.
We used microarray to determine the effect of Vascepa on hepatic gene expression in a diet induced obesity model.

overall_design: Livers were isolated from male C57BL/6 male mice treated with Vascepa for 7 days followed by high fat diet feeding for 6 weeks.

first: Michael

last: Wheeler


title: Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays [Expt2]

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 660 S Euclid Ave, Campus Box 8232

department: Genetics

institute: Washington University in St. Louis

summary: Using Massively Parallel Reporter Assays (MPRAs), we functionally screened over 1,000 SNPs, prioritized from 39 neuropsychiatric trait/disease GWAS loci based on overlap with predicted regulatory features—including expression quantitative trait loci (eQTL) and histone marks—from human brains and cell cultures. Using mouse neuroblastoma Neuro2a (N2a) cells, we identify over 100 SNPs with allelic effects on expression. Functional SNPs were enriched for binding sequences of retinoic acid-receptive transcription factors (TFs); with additional allelic differences unmasked in cells treated with all-trans retinoic acid (ATRA). Motifs overrepresented at functional SNPs corresponded to a set of TFs highly specific to serotonergic neurons and collectively downregulated in schizophrenia. Our application of MPRAs to screen MDD-associated SNPs suggested a shared transcriptional regulatory program across loci, a subset of which are unmasked by retinoids. Additional code and results corresponding to this GEO submission can be found at https://bitbucket.org/jdlabteam/n2a_atra_mdd_mpra_paper/src    Note that while paired-end sequencing was technically performed, only read 1 (i.e., the barcode-spanning read) of each pair was utilized for analysis, and thus only read 1 files are provided. (fastq files are processed as plain text using string-matching for stringent barcode identification, so header inconsistencies regarding single/paired end read design should not cause issues using our pipeline; however, if read 2 files are required to perform your own form of analysis, contact mulveyb@wustl.edu ; we are happy to provide them.)

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design:
n=6 replicates each of plasmid-transfected N2A cells, treated in culture with either 20µM all-trans retinoic acid (ATRA) or vehicle (100% DMSO).
Grants:
1. 5F30MH116654 - Bernard Mulvey - Identification and characterization of common, noncoding regulatory variants associated with Major Depressive Disorder - NIMH

2. 1R01MH116999 - Joseph Dougherty - Highly parallel analysis of 5' and 3' UTR variants in Autism Spectrum Disorders - NIMH

3. 571009 - Joseph Dougherty - Simons Foundation

first: Bernard

last: Mulvey

middle: D


title: Transcriptional-Regulatory Convergence Across Functional MDD Risk Variants Identified by Massively Parallel Reporter Assays [Expt1]

summary: Using Massively Parallel Reporter Assays (MPRAs), we functionally screened over 1,000 SNPs, prioritized from 39 neuropsychiatric trait/disease GWAS loci based on overlap with predicted regulatory features—including expression quantitative trait loci (eQTL) and histone marks—from human brains and cell cultures. Using mouse neuroblastoma Neuro2a (N2a) cells, we identify over 100 SNPs with allelic effects on expression. Functional SNPs were enriched for binding sequences of retinoic acid-receptive transcription factors (TFs); with additional allelic differences unmasked in cells treated with all-trans retinoic acid (ATRA). Motifs overrepresented at functional SNPs corresponded to a set of TFs highly specific to serotonergic neurons and collectively downregulated in schizophrenia. Our application of MPRAs to screen MDD-associated SNPs suggested a shared transcriptional regulatory program across loci, a subset of which are unmasked by retinoids. Additional code and results corresponding to this GEO submission can be found at https://bitbucket.org/jdlabteam/n2a_atra_mdd_mpra_paper/src

overall_design:
n=6 replicates of plasmid-transfected N2A cells, plated at 2 different densities at the time of transfection (linear regression showed that this had no effect on expression of any barcode set).
Grants:
1. 5F30MH116654 - Bernard Mulvey - Identification and characterization of common, noncoding regulatory variants associated with Major Depressive Disorder - NIMH

2. 1R01MH116999 - Joseph Dougherty - Highly parallel analysis of 5' and 3' UTR variants in Autism Spectrum Disorders - NIMH

3. 571009 - Joseph Dougherty - Simons Foundation


title: Genome-wide map of MAZ transcription factor in primary human erythroid cells

city: Midlothian

first: Douglas

last: Vernimmen

address: The University of Edinburgh, Easter Bush Campus, Midlothian

department: Roslin Institute

institute: University of Edinburgh

summary: We report the distribution of binding sites of Myc-associated zinc finger (MAZ) transcription factor in primary human erythroid cells

overall_design: MAZ was pulled down using anti-MAZ antibody (Bethyl Laboratories (A301-652A)) from chromatin of primary human eyrthroid cells

first: Darya

last: Deen

first: David

last: Garrick


title: IgG1 Immune Complexes Inhibit Naïve T Cell Proliferation but Stimulate a Subset of Their Progeny

status: Public on Jun 26 2021

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

summary: We examined the effects of well-defined, soluble IgG1 immune complexes on the phenotypes of human peripheral naive CD8+ T cells. We demonstrate that IgG1-ICs inhibit the proliferation and differentiation of one subset of naïve T cells but stimulate the division of another naïve-like subset. We utilize RNA-Seq to characterize the inhibited and stimulated T cell subsets.

overall_design: (1) Well-defined immune complexes (ICs) were formed using trinitrophenol-conjugated bovine serum albumin (TNP-BSA; 25-35 TNP-moieties/BSA molecule) as the antigen and monoclonal anti-trinitrophenol IgG1 antibodies to form TNP-BSA-anti-TNP IgG1 ICs. Additionally, we generated ICs (Fc5 IgG1 ICs) comprising an engineered aglycosylated IgG1 Fc (Fc5 IgG1) that selectively binds FcγRI with high affinity but presents no binding to all other FcγRs. (2) Proliferation experiments were set up for three unique human donors (017, 050, and 054) as described in the article methods section (Preparing T cells for In Vitro Functional Assays: Activation, IC-Incubation, and Culture). Briefly, CellTrace-labelled naïve CD8+ T cells were activated and incubated with 50μg/mL IgG1-ICs (017, 050, and 054; n=3) or Fc5 IgG1-ICs (017 and 054; n=2) in technical duplicates. Dynabeads were removed at t= 60 hrs. After 5.5 days in culture, IgG1-IC-treated T cells were sorted based on CellTrace fluorescence into two fractions: Inhibited T cells (InhT) and Stimulated T cells (StimT). Fc5-IgG1-IC-treated T cells (Fc5T) were not sorted and served as controls. (3) Total RNA was extracted from InhT, StimT, and Fc5T samples (N=16). RNA samples were then forward processed by the Genomic Sequencing and Analysis Facility (GSAF) at UT Austin. Briefly, mRNA was isolated (poly-A capture) and stranded libraries were created (dUTP Method; NEB NGS kit) for paired-end sequencing (PE75, NextSeq 500). If any replicate for a particular donor failed to create a quality library, GSAF equally amplified all samples from that donor (6 PCR cycles) and re-attempted library creation. (4) Bioinformatically, adapters were trimmed from the reads using Cutadapt and then aligned using HISAT to the human genome version hg38. Read counts were generated by FeatureCounts using parameters for fractional counting.

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